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Apply fails with single input file #123

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tnitka opened this issue Mar 20, 2024 · 2 comments · May be fixed by #124
Open

Apply fails with single input file #123

tnitka opened this issue Mar 20, 2024 · 2 comments · May be fixed by #124
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@jjacobson95

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@tnitka
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tnitka commented Mar 20, 2024

When running Apply with a single input file, Snekmer fails with the error message
InvalidIndexError in line 292 of /qfs/people/nitk592/snekmer-main/Snekmer/src/snekmer/snekmer/rules/apply.smk: Reindexing only valid with uniquely valued Index objects

It's currently possible to work around this issue by splitting the input into 2 or more fasta files.
@tnitka
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tnitka commented Mar 25, 2024

This error also sometimes occurs even if the input sequences are split into multiple files. This might be Snekmer reading the same name for two sequences, which shouldn't be happening here as each sequence is uniquely labeled by profmark.

@jjacobson95
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@tnitka would you be able to provide the same files you used? Haven't been able to reproduce this yet.

@tnitka tnitka linked a pull request Apr 23, 2024 that will close this issue
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Pin numpy to 1.22.3 in environment_BSF.yml and environment_Windows.yml PNNL-CompBio/Snekmer
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@jjacobson95 @tnitka